Complete programmable control over physical matter at the molecular scale implies examples such as the following:

An architect designs an office building on a computer. On completion, she merely has to tap a key--the building is constructed, molecule by molecule, by microscopic machines right before her very eyes.

With sufficient knowledge of the chemical compositions, one may easily turn any kind of biomass into food for the entire planet. See blue goo.

Nano-replacement: attach a tiny nanobot to each neuron in your brain; all inputs and outputs are monitored until the behavior can be perfectly predicted; kill every neuron; you are left (hopefully) with a fully functioning mind with merely a new physical substrate.

Each one of us is a word of approximately 700,000,000 characters, and this word is made flesh when the sperm and the egg form a zygote and the DNA textural message is downloaded into matter. Now we are on the brink of decoding the human genome, and the end result of this is that the flesh will be made word.